MOSAIC VARIANTS IN HEREDITARY CANCER GENES IDENTIFIED
ON NEXT GENERATION SEQUENCING PANELS
Jeffrey Bissonnette, MSc, CGC; Jessica L Mester, MS, CGC; Lisa R Susswein, MSc, MPH, CGC; Patricia D Murphy, PhD, FACMG; M. Laura Cremona, PhD, FACMG; Rachel T Klein, MS, CGC;
Kathleen S Hruska, PhD, FACMG
GeneDx, Gaithersburg, Maryland, USA
Background
Methods
• Mosaicism may be identified during genetic testing, when blood or other specimens are analyzed for germline
variants responsible for personal/family history of disease.
• We reviewed the clinical histories and test results of individuals who had BRCA1/BRCA2 or multi-gene
hereditary cancer panel testing at GeneDx who were mosaic for at least one variant that was identified by
Next-generation sequencing or by array CGH deletion/duplication analysis.
• Emerging data suggests that mosaic variants in genes associated with leukemia/lymphoma, including TP53
and ATM, can be present in peripheral blood samples from apparently healthy individuals prior to the diagnosis
of a hematologic malignancy.1-3
• Sequence variants were confirmed to be mosaic by Sanger sequencing. Array variants were confirmed either
by MLPA, qPCR, or repeat array CGH.
• Understanding whether mosaic variants are constitutional as opposed to somatic may impact the patient’s
future cancer risk as well as recurrence risks to family members.
• In some cases, results of testing for the variant in family members or in a second tissue from the proband were
also reviewed.
• An unpaired t-test was used to compare the allelic fraction of the mosaic sequence variants in individuals with
a personal history of cancer to those with no reported personal history of cancer.
Results
• Between October 2013 and February 2016, 143 instances of mosaicism were identified in 142 individuals
(Table 1).
• Testing of a second sample was performed in 3/142 (2.1%) probands for the mosaic variant initially identified in
blood.
• Fibroblast testing was negative in two cases, one for a TP53 mosaic variant and one for an ATM mosaic
variant.
• The mean allelic fraction for sequence variants was 17.5% and was not significantly different for patients with
(M=17.7%, SD=6.6) or without a personal history of cancer (M=14.8%, SD=4.5; t(124)=1.22, p=0.22).
• Testing of a buccal sample was negative for one case for a TP53 mosaic variant.
• All mosaic large deletions or duplications encompassed at least the entire gene (n=9).
• Four of 11 individuals with a previous history of leukemia/lymphoma had a mosaic large genomic deletion/
duplication detected by array CGH.
• The majority of the 41 individuals with a mosaic pathogenic or likely pathogenic variant in TP53 did not have
a history suggestive of Li-Fraumeni syndrome (Table 2). Among those meeting NCCN testing criteria, all had a
personal history of breast cancer diagnosed <31 years of age.
• Genes for which mosaicism was most often detected were ATM, CHEK2, and TP53 (Figure 1).
• Twenty five adult offspring of 17/142 (11.9%) individuals pursued targeted testing for a parent’s mosaic variant,
with none testing positive.
Table 1. Demographic Information
Figure 1. Biomarker Variants by Gene: Post Germline Confirmatory Testing
n (%)
Mean/Median (range)
Gender
Female
Male
Age
20-29
30-39
40-49
50-59
60-69
70-79
80+
Sample Type
Blood
Oral rinse
Personal/Family History
Personal history of cancer
Personal history of leukemia/lymphoma
No reported personal history of cancer
Family history of cancer
No reported family history of cancer
Ancestry
Caucasian
Ashkenazi Jewish
African American
Hispanic
Multiple
Unknown
Table 2. Patients with Mosaic Pathogenic/Likely
Pathogenic TP53 Variants (N=41)
60
134 (94.4%)
8 (5.6%)
n (%)
54
63.8/64 (26-95)
4 (2.8%)
4 (2.8%)
12 (8.5%)
26 (18.3%)
47 (33.1%)
32 (22.5%)
17 (12.0%)
131 (92.3%)
11 (7.7%)
132 (93.0%)
11 (7.8%)
10 (7.0%)
140 (98.6%)
2 (1.4%)
110 (77.5%)
9 (6.3%)
4 (2.8%)
4 (2.8%)
5 (3.5%)
10 (7.0%)
Testing/Diagnostic Criteria
50
40
Met NCCN TP53 testing criteria
5 (12.2%)
Met Li-Fraumeni diagnostic criteria
0 (0%)
Met Chompret testing criteria
0 (0%)
33
30
26
Familial Testing
20
1 or more children negative
for variant
Other Pathogenic/Likely
Pathogenic Variants
10
4
0
1
APC
ATM
4
3
4
1
2 1
BRCA1 BRCA2 CDH1 CHEK2 MSH2
■ NGS
1
MSH6
11 (26.8%)
2
NBN
1
1
PALB2 POLE
1
PTEN
3
1
STK11
■ Array
TP53
Heterozygous for pathogenic
BRCA1/BRCA2 variant
3 (7.3%)
Mosaic for two pathogenic
TP53 variants
1 (2.4%)
Conclusions
• In this series, while the data is still limited, clinical histories of individuals with TP53 pathogenic/likely pathogenic
mosaic variants, fibroblast testing, and familial testing results suggest these variants are unlikely to be present
in the germline.
• Since recent studies have suggested a future risk for hematologic malignancy in individuals with somatic
variants in genes associated with leukemia/lymphoma1-3, testing for the mosaic variant in other tissues may aid
in assessing whether the variant is likely somatic, which may indicate that closer follow-up is warranted.
References
1.Genovese G et al. N Engl J Med. 2014 Dec 25;371(26):2477-87.
2.Jaiswal S et al. N Engl J Med. 2014 Dec 25 371(26):2488-98.
3.Xie M et al. Nat Med. 2014 Dec;20(12):1472-8.
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